Infiltration
by MacGateFan
Summary: He's the contingency plan for the occurrence in Critical Mass. His mission: Kill the leaders of the Atlantis Expedition. No Ships. Sheppard and Weir whump.


Title: Infiltration

Rating: PG-13

Author: MacGateFan

Timeline: After Critical Mass

Disclaimers: All characters belong to people who aren't me.

* * *

He had infiltrated into Atlantis with ease. Even after the previous incident with Colonel Caldwell and his Goa'uld. Obviously that hadn't prepared themselves for him. He was told the expedition leaders needed to be taken out and their own leaders would take over in those positions.

One person in particular stood out, he was the military leader. To be honest, the man never thought his cousin would ever be promoted, especially after that stunt in Afghanistan. Who knew that relocation to Antarctica could change one's career path?

Jared would never believe John changed it on his own. No, Weir had much to do with it. She petitioned for his cousin to come out here. However the main reason for him doing this was something neither could ever understand.

Jared quietly entered Weir's quarters. From what he could pick up over the radio, she was turning in for the evening...

Elizabeth sighed as she headed to her quarters. Now that the threat from the Goa'uld was gone, she could attempt to relax. She could only imagine what Colonel Caldwell must be feeling right now. The thought made her shudder.

The minute she entered her quarters, Elizabeth knew something was wrong. She barely had a chance to activate her radio when a hand snaked around her neck. Elizabeth struggled in the grasp, feeling dizzy as her air supply was cut off.

"Stop moving, Dr. Weir," the unknown voice rasped in her ear. "Call Colonel Sheppard or I will detonate a bomb to go off in the control room. Tell him to meet you here. Oh, and make sure he comes alone."

Elizabeth took a deep breath once he loosened his hold on her. "Who are you?" she asked, attempting to turn around.

He made certain she wouldn't see his face. "No one you need to concern yourself with. Now call Colonel Sheppard!"

Elizabeth nodded slowly, worried about what this man was capable of. She wasn't going to doubt him about the bomb because if he could make it to Atlantis and her quarters undeterred, she knew he meant business. The business of The Trust.

"John, this is Elizabeth. Could you meet me in my quarters, please? There's something we need to discuss."

_"On my way."_

Elizabeth left the radio on but before she could say anything, he snatched it from her ear and smacked her in the head with his 9mm. Darkness surrounded Elizabeth as she fell to the floor.

* * *

John was heading to the mess hall when Elizabeth's call came. He figured she forgot to tell him something regarding their debriefing. Why she just didn't wait until morning, he didn't know.

John rang the door chime and it was a couple of minutes before it opened. Finding Elizabeth unconscious on the floor was not something he was expecting. He immediately rushed to her side, checking for a pulse.

He sighed in relief when he found it, strong and steady. John heard the sound of the safety being removed from a 9mm. Just as he was about to reach for his own, the other went off.

"Sorry, John," Jared said as he watched his cousin drop to floor.

John stared at the blood in shock, then up at the man before him. What the hell was going on? However, John wasn't going to get answers anytime soon as the man ran out the door.

"Jared," he gasped out, attempting to catch his breath.

Elizabeth woke up a moment later. She heard the sound of painful breathing next to her and turned to see John lying on the floor, clutching his chest. She immediately sat up, looking all over for her radio.

Since she couldn't find hers, she reached for John's. "This is Weir. I need a medical and security team to my quarters ASAP!"

_"Elizabeth?"_ Carson replied.

"Carson, John's been shot."

_"Bloody hell," _he exclaimed. She could hear him ordering his staff around._ "Okay, Love, can you tell how bad it is?"_

"I-I don't know. There's blood everywhere and it's coming from the left side of his chest. He seems to be having trouble breathing and although he's conscious, he won't respond to me.■

_"Elizabeth, I know it's not easy, but you need to stay calm for Colonel Sheppard. Just make sure to keep the airway open and clear."_

She nodded, almost forgetting Carson wasn't with her yet. "Okay. I'm using my jacket to control the bleeding."

"Lizabeth?"

"John?"

"Hurts...Jar..."

"I know it does, John, just rest. Carson is on his way."

* * *

Carson arrived at Elizabeth's quarters just as Major Lorne's team did. "Doc, what's going on?"

"Not sure exactly, Major. I just know that Colonel Sheppard was shot so I need to get my team in there."

Lorne nodded. "Go ahead. We'll check out the immediate area."

A few minutes after Carson entered her quarters, Elizabeth emerged with a nurse looking quite ashen in comparison to the crimson red blood on her hands and shirt. Evan knew the signs of shock and took his jacket off to wrap it around her shoulders.

"Ma'am?"

"We have a security breech, Major. Make certain the control room is secure and non-essential personnel are confined to quarters for the time being. I expect you to make this your top priority!" Elizabeth paused. "And contact Colonel Sheppard's team to let them know what happened."

Lorne nodded as she was led to the infirmary. "Control this is Major Lorne, contact Ronon and Teyla on the mainland and apprise them of the situation. And do we know when Dr. McKay will be back with Captain Anderson's team?"

_"They're schedule to arrive at 1500 hours, Major,"_ Chuck replied.

"Let him know what's going on the minute he arrives."

"Will do."

Lorne took a deep breath and since Dr. Weir's quarters were clear of the med team, he took two of his men and entered to make an assessment of the situation.

* * *

Rodney sent an evil glare back at the two scientists behind him. The two were still arguing over how the electrical system of this Podunk town could go haywire. "Gee," Rodney had said, "let me guess. Two words: Podunk. Town."

He was really only doing this as a favor to Elizabeth because right now he could be enjoying salsbury steak in the mess hall with Sheppard. Rodney was half tempted to hug Captain Anderson in excitement when they reached the DHD.

Rodney's dream of salsbury steak was short lived when he entered the Gateroom. It was quiet and no one was around to greet them. Not even Elizabeth. Rodney was about to head to the infirmary when Chuck called him upstairs.

"There's been an incident. Colonel Sheppard was shot."

"What?" Rodney asked, staring at the man in shock. This had to be a joke, right? But the look on Chuck's face told him it was no joke. "How the hell did that happen?"

Chuck merely shrugged. "Major Lorne is looking into it. Dr. Weir and the rest of your team are in the infirmary."

Rodney needed no further urging to get down there. Upon arrival he found everyone in various states of worry. Teyla was seated on one of the beds meditating and Ronon was pacing back and forth like a caged cat.

Elizabeth had him more concerned. She was also on an infirmary bed, but from the look of the bandage on her head, he knew she'd been injured as well. Rodney was about to walk over to her when Ronon realized he was standing there.

"McKay."

"What the hell happened?"

Elizabeth's eyes opened when she heard Rodney's voice. She slowly sat up, wincing as the movement caused her head to pound even more. "We have a problem, Rodney," she said.

Rodney listened in stunned silence as Elizabeth filled him in on what happened. Whoever this guy was would pay. Rodney would make him pay by sending Ronon after him. And he knew Ronon would be happy to oblige.

"How long has Carson... you know?" Rodney asked, glancing at OR.

"Too long in my opinion," Ronon replied.

Elizabeth took a deep breath. "He was shot in the chest. I heard them mention something about the possibility of a collapsed lung."

"Looks like we'll be fine about that," Carson said, heading towards them. "Colonel Sheppard is stable and resting comfortable. He's rather lucky that the bullet didn't travel far."

"Lucky," Rodney scoffed. "Lucky would be him waking up and IDing the lunatic we have running around the base. I mean, can't we enjoy a second of quiet around here? Especially after that Goa'uld in Caldwell thing!"

Ronon nodded. "He's right. We need to find out who this guy is and make sure he doesn't try to kill Sheppard again."

"Elizabeth, can you remember anything of this man?" Teyla asked.

By this time, Elizabeth was sitting on the edge of her bed, legs dangling over the side. Carson had made his way to her, checking her pupils and vitals. "Just that it was a man and he was very strong. I didn't recognize his voice."

Carson saw that Elizabeth paused, waiting for his diagnosis. "Aye, you can leave. I know that you have a lot of work to do and you need to contact the SGC. I'll keep you informed of the Colonel's condition."

* * *

John hated getting shot. Who wouldn't? However that wasn't his top priority when he woke up. No matter how much his chest was killing him, he needed to find someone and tell them who tried to kill him.

He still couldn't believe his cousin was in Atlantis. How Jared came to be here without him knowing, he wasn't sure. Maybe he changed his last name because John never saw it on the list of arrivals from the Daedalus and never heard his name mentioned.

John remembered the summer when he was 16. Jared was 14 at the time and the two were inseparable. They took John's Dad's corvette for a joy ride... without the man knowing... Needless to say the long red scratch on the side of said vehicle drained John of his allowance for nearly two months.

The cousins had laughed about it for years after, but John lost touch with Jared when he arrived in Afghanistan. The last time John spoke with him was just before he was shipped out to Antarctica. Jared had apparently taken his Father's side on the matter.

The two never laughed about their exploits again and this saddened John more than the fact that his cousin tried to kill him.

"Colonel?"

John blinked, looking over at Carson. "How long have you been standing there?"

"Long enough to see that you were deep in thought. What's troubling you, Son?"

He took a deep breath. "I know who we're looking for."

Carson immediately stopped taking John's vitals and called for his team along with Elizabeth and Lorne to meet them in the infirmary. The all stood crowded around his bed now waiting to see who he was going to reveal as the attacker.

"Well?" Rodney asked. "Who was it?"

"Yeah. I need to know who I'm going to beat to a pulp," Ronon added.

Teyla eyed him in concern. "John, you know this man well," she stated.

"I do. He's my cousin."

Rodney was stunned to say the least. He could tell the others were too. "What? I mean, are you sure?"

He nodded. "There's no mistaking Jared Michaels."

"But there is no Jared Michaels, John," Elizabeth replied. "At least not that I recall. Besides how could you have not seen him on the base?"

Ronon answered that. "If people don't want to be seen, they'll make themselves scarce."

John looked up at Lorne. "Anything, Major?"

"The only thing we know for certain, Sir, is that he was able to get into one of the armories and steal a 9mm. From there he headed to Dr. Weir's quarters and waited for her there."

Carson could see this information was beginning to agitate John. Maybe not by the man's expression, but by the machines all around him. Besides, he had been without his nasal cannula for long enough.

"Colonel," Carson said. "That's enough for right now. The only thing you should be concentrating on is getting rest."

"Yeah, right," Rodney muttered. Carson gave him a look and the scientist shut up. "So, Sheppard, we'll check into this. Don't worry about a thing!"

Teyla smiled. "Rodney is right, John. We will do everything in our power to find Jared."

John glanced at Elizabeth, then pulled Lorne aside as the others gave their well wishes and promises to visit. "Major, I know Elizabeth isn't going to like this, but I want two guards on her 24/7! She is not to be left alone under any circumstance unless she's in her quarters."

Lorne nodded. "I'm on it, Sir."

* * *

"Lieutenant Forrester." Jared looked up, nearly forgetting that was his alias. People tended to just leave him be. He stood at attention and saluted. "Major Lorne, Sir."

"I need you to stay with Dr. Weir like glue. Marks will be meeting you in her office shortly. She does have a few requests but your main objective is to keep her safe. These orders are per Colonel Sheppard. Understood?"

Jared hid the grin that wanted to burst. "Yes, Sir!"

"Good, dismissed."

Jared turned and headed down the hallway. He couldn't have made this any easier himself. Soon Dr. Weir would be out of the picture and the only one he'd have to deal with was John. Damn him and his ability to survive anything!

He arrived in the control room ten minutes later to see Marks already in Weir's office. Jared stood at attention just in the doorway. "At ease, Lieutenant," Elizabeth said.

"Ma'am," he replied.

"I was just telling Lieutenant Marks here that although I'm not happy about having guards for the next couple of days or so, I do appreciate it. That being said I feel I should tell you both what's led up to my needing guards in the first place."

Jared listened mostly because he wanted to know what everyone else knew. Of course John had already mentioned that they were cousins. He was really going to have silence him for good!

About an hour into guard detail Jared was ready to pull out his hair. The Trust were expecting results within the next few hours and he was stuck protecting Weir instead of killing her.

When he didn't think he could take it anymore Elizabeth stood up, stretched and walked over to the door. "I apologize, gentlemen. I should have offered you something to drink or a chair to sit in."

"Not to worry, Ma'am," Marks replied. "We're used to this kind of thing. Where we headed?"

Elizabeth smiled. "Thank you, Lieutenant. I was going to head to my quarters to get something."

"Lead the way."

Jared decided this would be his opportunity. Once they reached Elizabeth's quarters, he stopped her from opening the door. "If you don't mind, Dr. Weir, I should probably sweep the room before you go in."

"Of course, Lieutenant, thank you. I certainly don't want a repeat of last time."

Elizabeth and Marks stood outside her quarters for a good ten minutes before Jared appeared. "All clear, Doctor."

Jared moved away from the door, unnoticed by Elizabeth or Marks. The moment she entered the room, an explosion erupted. Elizabeth flew back into Marks and the pair landed in an unceremonious heap in the corridor. Neither were moving.

* * *

A loud explosion and alarms blaring woke John up from his peaceful slumber. He sat up, wincing at the sudden pain. Once it had settled he saw that the infirmary was in total chaos. Nurses were running all over the place gathering equipment and Carson was nowhere to be seen.

"Major Lorne to section 51B! Major Lorne!"

John's eyes widened in realization. That's where Elizabeth's quarters were. That meant only one thing. Jared had struck again. John ripped out his IV and tossed the nasal cannula to the side. He was probably going to be in a lot of pain later, but his city was under attack and he was going to stop it no matter what!

John rushed to his quarters to change and grab his weapon. As soon as he was ready, he ran out the door, only to run straight into his cousin. "Jared."

"John," the man replied with a grin. "How's life treating you?"

"What the hell are you doing?" John asked, aiming his 9 mm at Jared. "Where's Elizabeth?"

Jared seemed to look thoughtful for a minute. "Probably heading down to the infirmary. There was a huge explosion in her temporary quarters."

John's heart was beating wildly causing his chest to blossom into more pain, but he pushed it down, determined to talk Jared down. "You need to stop this," John said. "You're hurting innocent people!"

"Like you're so innocent, Cuz."

"I wasn't talking about me! What the hell are you doing working with The Trust?" he paused, fearing the worst. "You're not..."

"Hell no! You think I'd let one of those things burrow into my neck! No, they promised me something more important."

"What's that?" His cousin merely looked at the floor so John took a tentative step forward, pain now emanating from his chest. "Jared."

"Alyssa. They took my baby because of you!"

John closed his eyes and took as deep a breath as he could. True he hadn't seen her in years, but she had to be around 10 years old now. "God, Jared, I'm so sorry."

"You should be! They came after us once they realized we were related."

"Okay, fine, I can accept that it was my fault, but don't take it out on everyone here. These people don't deserve it."

Jared nodded. "Let's go for a walk, Cuz. Oh, and hand me your gun."

* * *

As soon as Elizabeth and Lieutenant Marks were situated, Carson headed over to Ronon, Teyla, and Lorne. "They're both going to be fine thankfully. Elizabeth has a mild concussion, nothing to be concerned about. We'll keep them here for observation over night, though."

Rodney rushed over to the four, out of breath. "Where's Sheppard?"

"Rodney, what are you on about, Colonel Sheppard is..." Carson trailed off noting the empty bed and IV pole lying on the floor. "Bloody hell!"

Lorne was about to follow them when his radio beeped. "Go ahead. Where? On my way. Have Alpha team meet there in five."

"Major?" Teyla asked once he was finished.

"The Colonel's cousin is holding him hostage on one of the lower south piers," he replied, rushing out the door.

Upon arrival they saw a very unstable looking guy, who was whole head taller than John, holding him at gunpoint. Rodney glanced nervously from one to the other. He saw John's hand up near his chest and a dark stain was spreading. His face looked unnaturally gray as well.

"We've got to do something!" Ronon growled.

Lorne nodded in agreement. "He's gotta know we're here now. Ronon, set your weapon to stun. I'll distract him by trying to talk him out of this."

"Got it."

Ronon moved into position as Lorne stepped closer to the door. "Stay right where you are Major," Jared said, his eyes still on John.

John coughed as he attempted to breath deeply. His chest wound was not helping the situation. Something was definitely wrong with this lungs right now. Pushing the pain down, he looked into his cousin's eyes, trying to find the words that would let him know he could save Alyssa.

"John, I'm sorry it's come down to this, but I love my daughter and I would do anything for her."

Pain emanated through his chest as John replied, "Jared, please! Let us help you! We have people on Earth who can help us get Alyssa back."

"Are you... are you sure?" Jared asked.

He loved his little girl and as was proved here, would do anything for her but at what cost? John was right, this wasn't going to help the situation.

John watched as Jared struggled with his thoughts. The fact that he had lowered his weapon was good enough for John so he stepped forward, reaching for the weapon. "Jared?"

Jared looked at him, eyes brimming with tears. "I'm sorry, John. So sorry. Tell Alyssa I'm sorry."

"What?" John thought he had a good grip on the 9mil but looking into Jared's eyes as it was discharged, he knew he didn't. "No!" he exclaimed as the two fell to the ground.

Jared coughed, looking over at John. "Tell Molly and 'Lyssa that I love them and that I'm so sorry."

Tears fell unnoticed down John's face as he held Jared's hand. "I will," he said, "I promise."

Jared smiled sadly as he closed his eyes for the last time.

John just sat there, staring at his cousin in complete shock. Everything was spinning around him and he could have sworn he heard Carson calling his name. However he didn't care at the moment and allowed the darkness to overtake him.

* * *

"Rodney, what are you doing?"

"Just trying to make sense of your voodoo," he replied, reading John's chart.

Carson came up behind him, arms crossed. "And what have you determined, Rodney McKay, MD?"

"Please, don't even associate my name with those letters!"

"I'll take that, thank you," Carson replied, snatching the chart. "Now if you don't mind, I need to check my patient's vitals. Don't you have important work to be doing?"

Rodney nodded. "Yes, very. However, I'll leave you to the most important person in Atlantis, though."

Carson stared after the scientist in shock. Even though Rodney was right, he was pretty sure he never heard him say something like that before. In fact, it was usually Rodney who thought he was the most important person in Atlantis.

"Um, Carson..." Rodney said, popping his head back in. _Didn't take him long,_ the physician thought. "Don't tell Sheppard I said that."

He chuckled as Rodney left again and turned to see a smirk on his patient's face. "Well, Colonel, I suppose that's something that needs to be preserved for posterity, don't you think?"

"Definitely."

"Okay, now I want the truth. How are the inhalation techniques working for you? Do they seem to be helping?"

John nodded. "I'm feeling much better, Carson." Physically, he added to himself.

Carson could tell John was still upset by what happened. He would be heading to Earth as soon as he was able to notify his cousin's wife concerning what happened to her husband. The young girl had, thankfully, been returned to her Mother unharmed.

"We'll do a chest x-ray before we leave to be certain, but your vitals are back to normal. I'm going to put you on light duty for now and we'll reassess your situation when we get back to Atlantis."

John raised an eyebrow. "We?"

"Oh no! Don't think I'm letting you go back to Earth without me in your condition! I don't care how well you feel!"

"I won't be alone, ya know, Doc. Rodney's coming with me," John replied.

Carson smiled. "Hence the reason I'm coming as well."

* * *

The debriefing on Earth had been a long process. Even though she wasn't originally due to be at the same debrief as John and Carson, Elizabeth went anyway. She wanted to get this whole mess over with.

She was heading to her quarters when she saw Rodney pacing in front of John's. "Rodney?"

"Huh? Oh, hey," he replied. "I was just waiting for him. We were supposed to go to his cousin's house to, you know..."

Elizabeth nodded. She hated that this had to happen. From what little she could gather about John's past, it seemed the only one who had shown any interest in his life was Jared. He had told her about the trouble they used to get themselves into.

Carson ended up walking by just then. "Rodney, what are you still doing here?" he asked.

"Waiting for Sheppard, who has yet to come out here if I may add."

"He left an hour ago!" Carson replied.

Elizabeth took a deep breath. "He went to talk to Jared's family alone?"

"I can't believe it!"

"Rodney," Carson said, "Calm down. If Colonel Sheppard felt he needed to do this alone, then we should respect that. He is a very private person after all."

* * *

John felt bad leaving Rodney, but this was something he had to do on his own. This was his family and no matter how much he wanted to avoid them, they had a right to hear what happened (the edited version of course) from him.

He counted to ten and rang the doorbell. John had to smile when he heard Alyssa's voice exclaiming that she was getting the door. When she opened, she squealed. "John!"

"Hey sweet girl," he replied, grabbing her as she launched herself into his arms. "You've gotten so big."

Alyssa nodded. "Daddy's says I'm gonna be taller than Mommy!"

"Maybe," he said. John looked up when he heard footsteps. Molly was standing there holding a baby. "Hey."

Molly smiled at him, but he could tell it didn't reach her eyes. He had a feeling she knew why he was there especially since they hadn't seen each other in years. "Come in, John."

The baby in her arms immediately held her pudgy hands out towards him. "Hold!" she demanded.

"Yes, Ma'am!"

"That's my little sister, Rose," Alyssa said proudly.

Molly bent down to address her daughter. "Sweetheart, John and I need to talk about grown up stuff right now. Could you go up to your room and play. I promise we won't be long."

Alyssa looked back and forth at them, then at Rose. "But what about her?"

"I'm going to lay her down for a nap in a minute. Go on upstairs." Once Alyssa was out of earshot, Molly stood up. "John? He's dead, isn't he? I knew it! I knew it the minute Alyssa came home unharmed. I knew he should have gone to the police, or at least tried to contact you!"

John wrapped his arms around Molly as she cried. "I am so sorry this happened!"

After a few minutes, Molly wiped her eyes and gently pulled away from him. "No," she said. "You are not going to blame yourself for this, John! You didn't do anything wrong. I knew Jared was up to something when he said he had to go out of town for a few days. I just didn't think..."

Before John could reply, Alyssa came down the stairs. "John! You really should..." she trailed off, seeing the tears on her Mom's face. "Mommy? You okay?"

"I can... I mean, if you need a minute."

"Please?" she asked. At his nod, she left the room with Rose.

"Come here, Lyss," he said, patting the seat next to him. "I have to tell you something."

She looked at him with curious eyes. "What's going on, John? Why is Mommy crying? What happened?"

"It's about your Dad, sweetheart."

John took a deep breath, not having the first clue how to break the news of a Father's death to his 10 year old daughter. He wondered if Molly shouldn't do this after all.

"John?" He turned to look at Alyssa, who had placed a hand on his arm. "Daddy's gone, isn't he?"

"Yeah, Lyss. He is, but wanted me to tell you something important."

"What's that?"

"He loves you very much and he's so sorry that he won't be here anymore."

Alyssa nodded. "I know he loves me, John. Wanna know how?"

"Sure."

"Because he's right here," Alyssa replied, patting her chest. "In my heart."

* * *

John was emotionally drained by the time he returned to the SGC. All he wanted to do was lie in his quarters and not deal with anyone until the funeral in a few days. Of course, lately John never seemed to be able to get his way.

"Rodney," he said with a sigh. His friend was standing in front of the door to his quarters. "What are you doing?"

"Just wanted to make sure you were all right," he replied.

John nodded, moving him out of the way. "Just great."

"Why can't you let someone help you for a change?"

John paused, halfway in the room. "I guess it's just been so long since I've had anyone to help me," he replied, voice barely above a whisper.

"You do now, John," Rodney told him. Instead of letting him answer, Rodney left him alone to his thoughts.

John stood there for the longest time before he finally shut the door and laid down on the bed. He was asleep the minute his head hit the pillow, although he certainly didn't feel like it when woke up to someone knocking on his door.

John slowly got up, shaking away the cobwebs, and wincing as a twinge of pain radiated from his chest. Glancing at the clock he saw he was due for pain meds. "Hey, Carson," he said, once he opened the door. "Nice timing."

Carson smiled. "I figured as much. Elizabeth should be by shortly with some dinner." There was silence as Carson checked John's vitals and gave him his medicine. "Are you feeling all right? I mean, I'm sure you've talked to enough people today, but..."

John nodded. "I'll be fine, Carson, but thanks."

Another knock brought Elizabeth and Rodney, both carrying trays full of food. Rodney sat at the table and immediately dug in. He looked up when he felt all eyes on him. "What? I'm hungry! You know I have to watch out for a hypoglycemic reaction."

John shook his head. "Some things never change."


End file.
